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2007 Annual Science Report

University of California, Berkeley Reporting  |  JUL 2006 – JUN 2007

Adaptation to Salinity in Microbial Communities

Project Summary

The potential relevance of evaporative lakes as analogs for the late stage hydrosphere of Mars (see results of Manga and collaborators in the UC Berkeley team) is well established (e.g., Benison and Laclair 2003, Astrobiology v.3).

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

Mechanisms of adaptation to high salt concentrations in evaporative lake systems

The potential relevance of evaporative lakes as analogs for the late stage hydrosphere of Mars (see results of Manga and collaborators in the UC Berkeley team) is well established (e.g., Benison and Laclair 2003, Astrobiology v.3). Based on findings of Benison and others, our NAI team identified Lake Tyrrell, Australia, as an important site in which to conduct studies of how organisms adapt to salinity extremes and to investigate the biomarker record of prior communities and their environments. Research began at the site in 2005. The objectives of this study are twofold. In the first instance, our goal is to study contemporary microbial communities with state of the art molecular methods so as to learn about biochemical mechanisms of adaptation and potential biomarkers from both cultivated and uncultivated lineages. This objective is described below. The second objective involves analysis of iron oxide concretions formed at spring sites in the lake and evaluation of potential mineralogical and organic biosignatures they may contain. This objective is described elsewhere (see iron sulfur system report).

Molecular studies of microbial adaptation in hypersaline environments

Motivated by the availability of some preliminary metagenomic data from planktonic microbial communities as the result of the Global Ocean Survey (Craig Venter and collaborators, 2007), we formed a collaborative team and requested funds for extensive genomic sequencing of microbial communities from Lake Tyrrell. NSF funded about 1.6 Ga bases of sequencing in 2006. Samples of planktonic consortia and biofilms were collected in January and August 2007. Libraries have been constructed for three samples (0.1 and 0.8 μm fractions) and initial sequence data indicates strong dominance by a relatively tractable number of organism types. As described previously, our expectation is that, with sequencing available, we will be able to achieve near complete genomic sampling for all populations that comprise > ~4% of the community. Given the availability of a number of isolate genomes from hypersaline adapted bacteria and archaea, it will also be possible to conduct extensive analysis of data from less highly sampled populations. In addition to searching for biochemical pathways that contribute to osmoregulation, our goal is to test the hypothesis that adaptation to gradients and salinity changes is achieved by selection for a subset of combinatorial genome types from a pool that arise via homologous recombination. Within this genome pool, variants are predicted to represent subtly different optimizations. The approach builds upon methods developed in community genomic studies of acid mine drainage consortia (see iron sulfur system section).

In the past year, emphasis has been placed on preliminary characterization of the consortia (e.g., 16S rRNA gene clone library based analysis of microbial biofilms (air-water interface and sediment surface mats, planktonic consortia, and communities captured in salt crystals). Results indicate that consortia are dominated by populations of archaea and bacteria closely and distantly related to known halophiles. Cultivation-based studies have also been conducted and many isolates are now on hand for future characterization. The main accomplishment of the past year centered around three large field trips that targeted sample collection for the proposed and planned molecular studies. Figure 1 illustrates filters with associated bacterial and archaeal cells used for library construction. Samples were collected simultaneously for characterization of bacterial-archaeal consortia, viruses, and lipids/pigments. The genomic work is in collaboration with Drs. Eric Allen and Karla Heidelberg, and astrobiology colleagues from Australia (see below). Lipid/pigment work is described below.

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A future objective of this study is to directly analyze microbial responses to salinity challenges via field and laboratory-based experiments. This can be achieved by using the genomic data from consortia as a foundation for identification and quantification of the complement of proteins produced by coexisting organisms. Community proteomes are characterized via mass spectrometry (two dimensional liquid chromatography-based MS/MS). We undertook a detailed analysis of genomic and existing proteomic data from a variety of systems in order to evaluate how divergence between the genomes of organisms present in samples used for proteomics and genomic degrade proteomic outcomes. The resulting publication (Denef et al. 2007) provides an important foundation for future work on Lake Tyrrell microbial consortia.

Lipid and pigment biomarker studies

A frontier for lipid / pigment biomarker research is supplementation of information about the genetic potential of cultivated organisms with information from uncultivated species. The lack of information for uncultivated organisms represents a large gap in knowledge that has potentially critical implications for analysis of molecules preserved in ancient rocks. Specifically, biomarkers in the rock record are assigned to specific lineages based on knowledge about the metabolic capabilities of modern organisms. However, currently uncharacterized organisms from other branches of the tree of life may be alternative sources of these molecules. For this reason, an objective of this project is to combine cultivation independent genomic analyses with cultivation independent lipid analyses. This work involves collaboration between our NAI team and Drs. Jochen Brocks (ANU) and Simon George (Macquarie University and Australian Center for Astrobiology) and is centered around Ph.D. research of UC Berkeley student Claudia Jones, who will work in part at ANU. Because this project is only relatively new, the primarily goals achieved in the past year are confined to sampling of biofilms and planktonic consortia and preliminary lipid studies of lake sediment cores. Results confirm the dominance by bacterial- and archaeal-derived biomarkers rather than eukaryotes. Figure 2 illustrates the biofilms sampled for genomic and lipid analysis.

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    Jill Banfield Jill Banfield
    Project Investigator
    Jochen Brocks

    Allen Eric

    Simon George

    Heidelberg Karla

    Eric Roden

    Brett Baker
    Research Staff

    Claudia Jones
    Doctoral Student

    Elliot Smith
    Undergraduate Student

    Objective 2.1
    Mars exploration

    Objective 3.2
    Origins and evolution of functional biomolecules

    Objective 4.1
    Earth's early biosphere

    Objective 5.3
    Biochemical adaptation to extreme environments

    Objective 7.2
    Biosignatures to be sought in nearby planetary systems